In the late 19th century the site where church now stands was a 20 acre estate known as Woodland Estate, with a bungalow at its centre in the heart of Kottayam. The property belonged to a foreign national, Mr. Hue Crafort, who sympathised with the growth of Christianity and sold the estate in Kolla Varsham 1064, Thula masam 24 (AD 1888) to the Nasraani Jaadhiyka Sangam (United Christian Group), a joint Christian fellowship led by His Holiness Pulikottil Joseph Mar Divannasios II and the Catholic priest Nidhirikkal Mani Kathanar. The tract was later known as the M. D. Seminary Compound.
His Holiness Pulikottil Joseph Mar Divannasios II proposed establishing an English school on the site. That proposal was opposed by the Catholic Church, which created a dispute and brought the Sangam’s activities to a halt. The Orthodox Church purchased Nidhirikkal Mani Kathanar’s share, and the whole property eventually came under the Malankara Orthodox Syrian Church.
In 1893 His Holiness Pulikottil Joseph Mar Divannasios II founded M. D. Seminary English School on the compound. The school grew over time into one of the leading educational institutions in the region. Desiring a chapel where students could worship, Thirumeni set aside a suitable area within the Woodland bungalow for that purpose.
The consecration (Koodasha) of the chapel was solemnized on 6 December 1896 in the blessed presence of Parumala St. Gregorios, the declared saint of the Malankara Church. At the behest of Parumala Thirumeni, the chapel was named Mar Elia Chapel, honoring the saint’s profound gratitude for divine protection. The name commemorates a pivotal moment during Thirumeni’s overseas journey, when a fierce storm threatened his voyage at sea. In that hour of peril, he attributed his safe passage to the intercession of Mar Elia (St. Elijah), and the chapel stands as a lasting tribute to that act of providence.